Job ID = 1300162 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:02:52 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T10:02:52 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T10:02:52 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T10:02:52 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-03T10:06:58 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 17,754,733 reads read : 17,754,733 reads written : 17,754,733 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:37 17754733 reads; of these: 17754733 (100.00%) were unpaired; of these: 393288 (2.22%) aligned 0 times 11873349 (66.87%) aligned exactly 1 time 5488096 (30.91%) aligned >1 times 97.78% overall alignment rate Time searching: 00:09:37 Overall time: 00:09:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1451096 / 17361445 = 0.0836 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Mon, 03 Jun 2019 19:25:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 19:25:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:25:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:25:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 19:25:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:25:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:25:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Mon, 03 Jun 2019 19:25:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:25:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:25:17: 1000000 INFO @ Mon, 03 Jun 2019 19:25:17: 1000000 INFO @ Mon, 03 Jun 2019 19:25:19: 1000000 INFO @ Mon, 03 Jun 2019 19:25:24: 2000000 INFO @ Mon, 03 Jun 2019 19:25:24: 2000000 INFO @ Mon, 03 Jun 2019 19:25:29: 2000000 INFO @ Mon, 03 Jun 2019 19:25:31: 3000000 INFO @ Mon, 03 Jun 2019 19:25:32: 3000000 INFO @ Mon, 03 Jun 2019 19:25:38: 4000000 INFO @ Mon, 03 Jun 2019 19:25:38: 3000000 INFO @ Mon, 03 Jun 2019 19:25:39: 4000000 INFO @ Mon, 03 Jun 2019 19:25:45: 5000000 INFO @ Mon, 03 Jun 2019 19:25:47: 5000000 INFO @ Mon, 03 Jun 2019 19:25:48: 4000000 INFO @ Mon, 03 Jun 2019 19:25:52: 6000000 INFO @ Mon, 03 Jun 2019 19:25:54: 6000000 INFO @ Mon, 03 Jun 2019 19:25:58: 5000000 INFO @ Mon, 03 Jun 2019 19:25:59: 7000000 INFO @ Mon, 03 Jun 2019 19:26:01: 7000000 INFO @ Mon, 03 Jun 2019 19:26:07: 8000000 INFO @ Mon, 03 Jun 2019 19:26:07: 6000000 INFO @ Mon, 03 Jun 2019 19:26:10: 8000000 INFO @ Mon, 03 Jun 2019 19:26:14: 9000000 INFO @ Mon, 03 Jun 2019 19:26:17: 7000000 INFO @ Mon, 03 Jun 2019 19:26:17: 9000000 INFO @ Mon, 03 Jun 2019 19:26:21: 10000000 INFO @ Mon, 03 Jun 2019 19:26:25: 10000000 INFO @ Mon, 03 Jun 2019 19:26:26: 8000000 INFO @ Mon, 03 Jun 2019 19:26:28: 11000000 INFO @ Mon, 03 Jun 2019 19:26:32: 11000000 INFO @ Mon, 03 Jun 2019 19:26:35: 12000000 INFO @ Mon, 03 Jun 2019 19:26:36: 9000000 INFO @ Mon, 03 Jun 2019 19:26:39: 12000000 INFO @ Mon, 03 Jun 2019 19:26:42: 13000000 INFO @ Mon, 03 Jun 2019 19:26:46: 13000000 INFO @ Mon, 03 Jun 2019 19:26:46: 10000000 INFO @ Mon, 03 Jun 2019 19:26:49: 14000000 INFO @ Mon, 03 Jun 2019 19:26:53: 14000000 INFO @ Mon, 03 Jun 2019 19:26:55: 11000000 INFO @ Mon, 03 Jun 2019 19:26:56: 15000000 INFO @ Mon, 03 Jun 2019 19:27:00: 15000000 INFO @ Mon, 03 Jun 2019 19:27:03: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:27:03: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:27:03: #1 total tags in treatment: 15910349 INFO @ Mon, 03 Jun 2019 19:27:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:27:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 19:27:03: #1 tags after filtering in treatment: 15910349 INFO @ Mon, 03 Jun 2019 19:27:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:27:03: #1 finished! INFO @ Mon, 03 Jun 2019 19:27:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:27:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:27:04: 12000000 INFO @ Mon, 03 Jun 2019 19:27:05: #2 number of paired peaks: 811 WARNING @ Mon, 03 Jun 2019 19:27:05: Fewer paired peaks (811) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 811 pairs to build model! INFO @ Mon, 03 Jun 2019 19:27:05: start model_add_line... INFO @ Mon, 03 Jun 2019 19:27:05: start X-correlation... INFO @ Mon, 03 Jun 2019 19:27:05: end of X-cor INFO @ Mon, 03 Jun 2019 19:27:05: #2 finished! INFO @ Mon, 03 Jun 2019 19:27:05: #2 predicted fragment length is 105 bps INFO @ Mon, 03 Jun 2019 19:27:05: #2 alternative fragment length(s) may be 4,105 bps INFO @ Mon, 03 Jun 2019 19:27:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.10_model.r WARNING @ Mon, 03 Jun 2019 19:27:05: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:27:05: #2 You may need to consider one of the other alternative d(s): 4,105 WARNING @ Mon, 03 Jun 2019 19:27:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 19:27:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:27:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:27:06: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:27:06: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:27:06: #1 total tags in treatment: 15910349 INFO @ Mon, 03 Jun 2019 19:27:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:27:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 19:27:07: #1 tags after filtering in treatment: 15910349 INFO @ Mon, 03 Jun 2019 19:27:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:27:07: #1 finished! INFO @ Mon, 03 Jun 2019 19:27:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:27:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:27:08: #2 number of paired peaks: 811 WARNING @ Mon, 03 Jun 2019 19:27:08: Fewer paired peaks (811) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 811 pairs to build model! INFO @ Mon, 03 Jun 2019 19:27:08: start model_add_line... INFO @ Mon, 03 Jun 2019 19:27:08: start X-correlation... INFO @ Mon, 03 Jun 2019 19:27:08: end of X-cor INFO @ Mon, 03 Jun 2019 19:27:08: #2 finished! INFO @ Mon, 03 Jun 2019 19:27:08: #2 predicted fragment length is 105 bps INFO @ Mon, 03 Jun 2019 19:27:08: #2 alternative fragment length(s) may be 4,105 bps INFO @ Mon, 03 Jun 2019 19:27:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.05_model.r WARNING @ Mon, 03 Jun 2019 19:27:08: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:27:08: #2 You may need to consider one of the other alternative d(s): 4,105 WARNING @ Mon, 03 Jun 2019 19:27:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 19:27:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:27:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:27:14: 13000000 INFO @ Mon, 03 Jun 2019 19:27:22: 14000000 INFO @ Mon, 03 Jun 2019 19:27:32: 15000000 INFO @ Mon, 03 Jun 2019 19:27:41: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:27:41: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:27:41: #1 total tags in treatment: 15910349 INFO @ Mon, 03 Jun 2019 19:27:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:27:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 19:27:41: #1 tags after filtering in treatment: 15910349 INFO @ Mon, 03 Jun 2019 19:27:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:27:41: #1 finished! INFO @ Mon, 03 Jun 2019 19:27:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:27:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:27:43: #2 number of paired peaks: 811 WARNING @ Mon, 03 Jun 2019 19:27:43: Fewer paired peaks (811) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 811 pairs to build model! INFO @ Mon, 03 Jun 2019 19:27:43: start model_add_line... INFO @ Mon, 03 Jun 2019 19:27:43: start X-correlation... INFO @ Mon, 03 Jun 2019 19:27:43: end of X-cor INFO @ Mon, 03 Jun 2019 19:27:43: #2 finished! INFO @ Mon, 03 Jun 2019 19:27:43: #2 predicted fragment length is 105 bps INFO @ Mon, 03 Jun 2019 19:27:43: #2 alternative fragment length(s) may be 4,105 bps INFO @ Mon, 03 Jun 2019 19:27:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.20_model.r WARNING @ Mon, 03 Jun 2019 19:27:43: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:27:43: #2 You may need to consider one of the other alternative d(s): 4,105 WARNING @ Mon, 03 Jun 2019 19:27:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 19:27:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:27:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:27:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:27:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:28:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:28:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:28:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.10_summits.bed INFO @ Mon, 03 Jun 2019 19:28:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2522 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:28:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:28:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:28:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.05_summits.bed INFO @ Mon, 03 Jun 2019 19:28:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4591 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:28:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:28:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:28:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:28:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801811/SRX4801811.20_summits.bed INFO @ Mon, 03 Jun 2019 19:28:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1257 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。